*Target (protein/gene name): NADH-dependent Enoyl-[acyl-carrier-protein] reductase *NCBI Gene # or RefSeq#: NP_216000.1 *Protein ID (NP or XP #) or Wolbachia#: *Organism (including strain): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Etiologic Risk Group (see link below): */ Disease Information (sort of like the Intro to your Mini Research Write up): Link to TDR Targets page (if present): http://tdrtargets.org/targets/view?gene_id=6263 Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.) Essentiality of this protein: Is it a monomer or multimer as biological unit ? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ): Multimer as biological unit; 4-mer
Complex of proteins?: Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): Druggability index of .7
Structure (PDB or Homology model) -- PDB # or closest PDB entry if using homology model: -- For Homology Model option: ---- Show pairwise alignment of your BLASTP search in NCBI against the PDB ---- Query Coverage: ---- Max % Identities: ---- % Positives ---- Chain used for homology:
Current Inhibitors: Expression Information (has it been expressed in bacterial cells): Purification Method : Image of protein (PyMol with features delineated and shown separately): *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): *length of your protein in Amino Acids Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website Molar Extinction coefficient of your protein at 280 nm wavelength: TMpred graph Image ( http://www.ch.embnet.org/software/TMPRED_form.html ). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only): *GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): ( link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol) -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences): **
*NCBI Gene # or RefSeq#: NP_216000.1
*Protein ID (NP or XP #) or Wolbachia#:
*Organism (including strain): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Etiologic Risk Group (see link below):
*/ Disease Information (sort of like the Intro to your Mini Research Write up):
Link to TDR Targets page (if present): http://tdrtargets.org/targets/view?gene_id=6263
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.)
Essentiality of this protein:
Is it a monomer or multimer as biological unit ? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ): Multimer as biological unit; 4-mer
Complex of proteins?:
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): Druggability index of .7
*EC#: 1.3.1.9
Link to BRENDA EC# page: http://www.brenda-enzymes.org/enzyme.php?ecno=1.3.1.9
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer/learning-center/assay-library/ec-number-iii.html
-- -or link (or citation) to paper that contains assay information
-- links to assay reagents (substrates) pages.
--- List cost and quantity of substrate reagents, supplier, and catalog #
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
---- Query Coverage:
---- Max % Identities:
---- % Positives
---- Chain used for homology:
Current Inhibitors:
Expression Information (has it been expressed in bacterial cells):
Purification Method :
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
*length of your protein in Amino Acids
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website
Molar Extinction coefficient of your protein at 280 nm wavelength:
TMpred graph Image ( http://www.ch.embnet.org/software/TMPRED_form.html ). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
( link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**